patchwork.copynumbers: Function plot allele-specific copy numbers of the genome

Description Usage Arguments Details Author(s) See Also

View source: R/patchwork.copynumbers.r

Description

Input data for this function should be assessed from any of the karyotype_chroms() plots. For example <yoursample>_karyotype.chr<1-22,X,Y>.png.

See argument details.

Usage

1
patchwork.copynumbers(CNfile,cn2,delta,het,hom,maxCn=8,ceiling=1,forcedelta=F,male.sample=F,male2femref=F)

Arguments

CNfile

The name and path of your copynumbers file, generated from patchwork.plot(). Example Myfile_copynumbers.Rdata.

cn2

The approximate position of copy number 2,diploid, on total intensity / coverage axis.

delta

The difference in total intensity between consecutive copy numbers. For example 1 and 2 or 2 and 3. If copy number 2 has total intensity ~0.6 and copy number 3 har total intensity ~0.8 then delta would be 0.2.

het

Allelic imbalance ratio of heterozygous copy number 2.

hom

Allelic imbalance ratio of Loss-of-heterozygosity copy number 2.

maxCn

Highest copy number to calculate for. Default is 8.

ceiling

Default is 1.

forcedelta

Default is FALSE. If TRUE the delta value will not be subject to small adjustment changes.

male.sample

Default is FALSE. If it is a male sample put TRUE here and it will handle the XY chromosomes better.

male2femref

Default is FALSE. If TRUE the sample is male but the reference you used is female. This will correct for this.

Details

1. Run the patchwork.plot correctly. This will generate <yourfile>_copynumbers.Rdata. 2. View your plots and decide the correct parameters for the other arguments of this function. 4. Run the function.

Author(s)

Markus Mayrhofer, [email protected] Sebastian DiLorenzo, [email protected]

See Also

patchwork.plot
subfunctions_copynumbers


patchwork documentation built on May 31, 2017, 2:54 a.m.